Computational Identification, Characterization and Analysis of Conserved miRNAs and their Targets in Amborella Trichopoda

Hajieghrari, Behzad; Farrokhi, Naser; Goliaei, Bahram; Kavousi, Kaveh

doi:10.4172/2153-0602.1000168

Cited by 6 publications

(1 citation statement)

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“…Among the conserved miRNAs identified in A. trichopoda, the miR407 family had three orthologs in A. thaliana, Zea may, and Gossypium hirsutum. Similarly, there were two orthologs for A. trichopoda miR417 with A. thaliana and Oryzae sativa (Hajieghrari et al, 2015). Relative to sorghum, proso millet and pearl millet are evolutionarily the closest species, with their supposed common ancestor dating back ∼27 Mya, followed by ∼8.3 Mya between pearl millet and foxtail (Singh et al, 2017).…”

Section: Conserved Mirnas Across Milletsmentioning

confidence: 99%

Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance

et al. 2020

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Millets are the strategic food crops in arid and drought-prone ecologies. Millets, by virtue of nature, are very well-adapted to drought conditions and able to produce sustainable yield. Millets have important nutrients that can help prevent micro-nutrient malnutrition. As a result of the adverse effect of climate change and widespread malnutrition, millets have attained a strategic position to sustain food and nutritional security. Although millets can adapt well to the drought ecologies where other cereals fail completely, the yield level is very low under stress. There is a tremendous opportunity to increase the genetic potential of millet crops in dry lands when the genetics of the drought-tolerance mechanism is fully explained. MicroRNAs (miRNAs) are the class of small RNAs that control trait expression. They are part of the gene regulation but little studied in millets. In the present study, novel miRNAs and gene targets were identified from the genomic resources of pearl millet, sorghum, foxtail millet, finger millet, and proso millet through in silico approaches. A total of 1,002 miRNAs from 280 families regulating 23,158 targets were identified using different filtration criteria in five millet species. The unique as well as conserved structural features and functional characteristics of miRNA across millets were explained. About 84 miRNAs were conserved across millets in different species combinations, which explained the evolutionary relationship of the millets. Further, 215 miRNAs controlling 155 unique major drought-responsive genes, transcription factors, and protein families revealed the genetics of drought tolerance that are accumulated in the millet genomes. The miRNAs regulating the drought stress through specific targets or multiple targets showed through a network analysis. The identified genes regulated by miRNA genes could be useful in developing functional markers and used for yield improvement under drought in millets as well as in other crops.

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Section: Conserved Mirnas Across Milletsmentioning

confidence: 99%

Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance

et al. 2020

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In silico screening and validation of different dehydrogenases to produce 2,3-butanediol in Bacillus subtilis

Asolkar,

Anju,

Kumar

et al. 2024

Biotechnol Bioproc E

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Computational Identifi cation of MicroRNAs and Their Transcript Target(s) in Field Mustard (Brassica rapa L.)

Hajieghrari

Farrokhi

Goliaei

et al. 2017

Iran. J. Biotechnol.

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Background Micro RNAs (miRNAs) are a pivotal part of non-protein-coding endogenous small RNA molecules that regulate the genes involved in plant growth and development, and respond to biotic and abiotic environmental stresses posttranscriptionally. Objective In the present study, we report the results of a systemic search for identification of new miRNAs in B. rapa using homology-based ESTs (Expressed Sequence Tags) analysis and considering a series of fi ltration criteria. Materials and Methods Plant mature miRNA sequences were searched in non-protein coding ESTs registered in NCBI EST database. Zuker RNA folding algorithm was used to generate the secondary structures of the ESTs. Potential sequences were candidate as miRNA genes and characterized evolutionarily only and if only they fi t some described criteria. Also, the web tool psRNATarget was applied to predict candidate B. rapa miRNA targets. Results In this study, 10 novel miRNAs from B. rapa belonging to 6 miRNA families were identified using EST-based homology analysis by considering a series of fi ltration criteria. All potent miRNAs appropriate fold back structure. Several potential targets with known/unknown functions for these novel miRNAs were identified. The target genes mainly encode transcription factors, enzymes, DNA binding proteins, disease resistance proteins, carrier proteins and other biological processes. Conclusions MicroRNA having diverse functions in plant species growth, development and evolution by posttranscriptionally regulating the levels of specific transcriptome so by effecting on their translation products. Research in miRNA led to the identification of many miRNAs and their regulating genes from diverse plant species.

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Computational Identification, Characterization and Analysis of Conserved miRNAs and their Targets in Amborella Trichopoda

Cited by 6 publications

References 50 publications

Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance

Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance

In silico screening and validation of different dehydrogenases to produce 2,3-butanediol in Bacillus subtilis

Computational Identifi cation of MicroRNAs and Their Transcript Target(s) in Field Mustard (Brassica rapa L.)

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